title: Metagenomic 16S rDNA Illumina tags are a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities.
abstract: Sequencing of 16S rDNA polymerase chain reaction (PCR) amplicons is the most common approach for investigating environmental prokaryotic diversity, despite the known biases introduced during PCR. Here we show that 16S rDNA fragments derived from Illumina-sequenced environmental metagenomes (mi tags) are a powerful alternative to 16S rDNA amplicons for investigating the taxonomic diversity and structure of prokaryotic communities. As part of the Tara Oceans global expedition, marine plankton was sampled in three locations, resulting in 29 subsamples for which metagenomes were produced by shotgun Illumina sequencing (ca. 700 Gb). For comparative analyses, a subset of samples was also selected for Roche-454 sequencing using both shotgun (m454 tags; 13 metagenomes, ca. 2.4 Gb) and 16S rDNA amplicon (454 tags; ca. 0.075 Gb) approaches. Our results indicate that by overcoming PCR biases related to amplification and primer mismatch, mi tags may provide more realistic estimates of community richness and evenness than amplicon 454 tags. In addition, mi tags can capture expected beta diversity patterns. Using mi tags is now economically feasible given the dramatic reduction in high-throughput sequencing costs, having the advantage of retrieving simultaneously both taxonomic (Bacteria, Archaea and Eukarya) and functional information from the same microbial community.
authors.affiliation: Department of Marine Biology and Oceanography, Institute of Marine Science (ICM), Spanish National Research Council (CSIC), Passeig Marítim de la Barceloneta, 37-49, Barcelona, ES-08003, Spain.
authors.forename: Ramiro
authors.initials: R
authors.lastname: Logares
authors.forename: Shinichi
authors.initials: S
authors.lastname: Sunagawa
authors.forename: Guillem
authors.initials: G
authors.lastname: Salazar
authors.forename: Francisco M
authors.initials: FM
authors.lastname: Cornejo-Castillo
authors.forename: Isabel
authors.initials: I
authors.lastname: Ferrera
authors.forename: Hugo
authors.initials: H
authors.lastname: Sarmento
authors.forename: Pascal
authors.initials: P
authors.lastname: Hingamp
authors.forename: Hiroyuki
authors.initials: H
authors.lastname: Ogata
authors.forename: Colomban
authors.initials: C
authors.lastname: de Vargas
authors.forename: Gipsi
authors.initials: G
authors.lastname: Lima-Mendez
authors.forename: Jeroen
authors.initials: J
authors.lastname: Raes
authors.forename: Julie
authors.initials: J
authors.lastname: Poulain
authors.forename: Olivier
authors.initials: O
authors.lastname: Jaillon
authors.forename: Patrick
authors.initials: P
authors.lastname: Wincker
authors.forename: Stefanie
authors.initials: S
authors.lastname: Kandels-Lewis
authors.forename: Eric
authors.initials: E
authors.lastname: Karsenti
authors.forename: Peer
authors.initials: P
authors.lastname: Bork
authors.forename: Silvia G
authors.initials: SG
authors.lastname: Acinas
mesh_terms: D001105:Archaea / Q000235:genetics; D001419:Bacteria / Q000235:genetics; D017931:DNA Primers / Q000235:genetics; D004275:DNA, Ribosomal / Q000235:genetics*; D054892:Metagenome; D056186:Metagenomics / Q000379:methods*; D016133:Polymerase Chain Reaction; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D017931:DNA Primers; D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S